Reading data from an UFF file
In this example we show how to read channel and beamformed data from a UFF (Ultrasound File Format) file. You will need an internet connection to download data. Otherwise, you can run the CPWC_UFF_write.m first so the file 'test01.uff' is in the current path.
by Alfonso Rodriguez-Molares alfonso.r.molares@ntnu.no 07.08.2017
Contents
Checking the file is in the path
To read data from a UFF file the first we need is, you guessed it, a UFF file. We check if it is on the current path and download it from the USTB server otherwise.
% data location url='http://www.ustb.no/datasets/'; % if not found data will be downloaded from here filename='test02.uff'; % checks if the data is in your data path, and downloads it otherwise. % The defaults data path is under USTB's folder, but you can change this % by setting an environment variable with setenv(DATA_PATH,'the_path_you_want_to_use'); tools.download(filename, url, data_path);
USTB download tool File: test02.uff URL: http://www.ustb.no/datasets//test02.uff Path: C:\Users\47456\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\USTB\data
Error using tools.download (line 113) The HTTP request failed with error 404 Error in CPWC_UFF_read (line 23) tools.download(filename, url, data_path);
Reading beamformed data
Now that the file is in the machine we can start loading data. The first would be to check what is in there with the uff.index function
uff.index([data_path filesep filename],'/',display);
We see there is a beamformed_data dataset with name b_data. Let us load it and plot it. There are two ways of reading data from file:
- we can define an object of the correct class and use the method read:
b_data=uff.beamformed_data();
b_data.read([data_path filesep filename],'/b_data');
- or we can use the function uff.read_object and let the function create the correct object class for us
b_data2=uff.read_object([data_path filesep filename],'/b_data');
Either way the result is the correct uff.beamformed_data
figure; h1=subplot(1,2,1) b_data.plot(h1,'object.read'); h2=subplot(1,2,2) b_data2.plot(h2,'uff.read object');
Reading channel data
There are also two other structures in the file: a uff.scan and a uff.channel_data objects. Let us read them both
%scan=uff.read_object(filename,'/scan'); channel_data=uff.read_object([data_path filesep filename],'/channel_data');
And let us beamform that data with USTB
mid=midprocess.das();
mid.dimension = dimension.both;
mid.channel_data=channel_data;
mid.scan=scan;
mid.transmit_apodization.window=uff.window.tukey50;
mid.transmit_apodization.f_number=1.0;
mid.receive_apodization.window=uff.window.tukey50;
mid.receive_apodization.f_number=1.0;
% beamforming
b_data=mid.go();
b_data.plot();
which matches the images we saw previously.
Reading once and for all
It is possible to load all the data in the file into matlab memory without having to access each dataset individually. It suffices to call the read method without parameters and...
vars=uff.read_object([data_path filesep filename]);
... we get all the objects in the file into a cell structure
vars{1}.plot();